chr5-66327805-G-A

Position:

• chr5-66327805-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000666197.1(ENSG00000251391):​n.382+4823G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,182 control chromosomes in the GnomAD database, including 2,357 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.10 (2357 hom., cov: 32)
• Consequence: ENST00000666197.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.128

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.329 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000666197.1	n.382+4823G>A		intron_variant, non_coding_transcript_variant
	ENST00000663200.1	n.371+9379G>A		intron_variant, non_coding_transcript_variant
	ENST00000665668.1	n.394+4865G>A		intron_variant, non_coding_transcript_variant
	ENST00000668388.1	n.393-1015G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.101 AC: 15418 AN: 152064 Hom.: 2348 Cov.: 32

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.0471

Gnomad AMR AF: 0.0531

Gnomad ASJ AF: 0.00807

Gnomad EAS AF: 0.00116

Gnomad SAS AF: 0.0224

Gnomad FIN AF: 0.00763

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00561

Gnomad OTH AF: 0.0749

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.102 AC: 15466 AN: 152182 Hom.: 2357 Cov.: 32 AF XY: 0.0978 AC XY: 7275 AN XY: 74408

Gnomad4 AFR AF: 0.334

Gnomad4 AMR AF: 0.0530

Gnomad4 ASJ AF: 0.00807

Gnomad4 EAS AF: 0.00116

Gnomad4 SAS AF: 0.0226

Gnomad4 FIN AF: 0.00763

Gnomad4 NFE AF: 0.00562

Gnomad4 OTH AF: 0.0741

Alfa AF: 0.0547 Hom.: 340

Bravo AF: 0.116

Asia WGS AF: 0.0490 AC: 170 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	1.6
DANN	Benign	0.26

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10515002; hg19: chr5-65623633;